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.S13 { border-left: 1px solid rgb(233, 233, 233); border-right: 1px solid rgb(233, 233, 233); border-top: 1px solid rgb(233, 233, 233); border-bottom: 1px solid rgb(233, 233, 233); border-radius: 4px; padding: 6px 45px 4px 13px; line-height: 17.234px; min-height: 18px; white-space: nowrap; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 14px;  }</style></head><body><div class = rtcContent><h1  class = 'S0'><span>Initialisation of conserved moiety decomposition</span></h1><div  class = 'S1'><span>Conserved moiety decomposition consists of several sequential live scripts</span></div><ol  class = 'S2'><li  class = 'S3'><span>tutorial_initConservedMoietyPaths.mlx   (this script)</span></li><li  class = 'S3'><span>tutorial_buildAtomTransitionMultigraph.mlx                                </span></li><li  class = 'S3'><span>tutorial_identifyConservedMoieties.mlx</span></li><li  class = 'S3'><span>tutorial_analyseConservedMoieties.mlx</span></li><li  class = 'S3'><span>tutorial_visualiseConservedMoieties.mlx     </span></li></ol><div  class = 'S1'><span>Define the model that will be used for conserved moiety decomposition</span></div><div class="CodeBlock"><div class="inlineWrapper"><div  class = 'S4'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">if </span><span >~exist(</span><span style="color: rgb(170, 4, 249);">'modelName'</span><span >,</span><span style="color: rgb(170, 4, 249);">'var'</span><span >)</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >    modelName = </span><span style="color: rgb(170, 4, 249);">'iDopaNeuro1'</span><span >;</span></span></div></div><div class="inlineWrapper outputs"><div  class = 'S6'><span style="white-space: normal"><span >    </span><span style="color: rgb(2, 128, 9);">%modelName = 'DAS'</span></span></div><div  class = 'S7'><div class="inlineElement eoOutputWrapper embeddedOutputsVariableStringElement" uid="58A7899F" data-testid="output_0" data-width="428" data-height="20" data-hashorizontaloverflow="false" style="width: 458px; max-height: 261px; white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div class="textElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><span class="variableNameElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;">modelName = </span>'DAS'</div></div></div></div></div><div class="inlineWrapper"><div  class = 'S8'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">end</span></span></div></div></div><div  class = 'S9'><span>Setup the paths</span></div><div class="CodeBlock"><div class="inlineWrapper"><div  class = 'S4'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">switch </span><span >modelName</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >    </span><span style="color: rgb(14, 0, 255);">case </span><span style="color: rgb(170, 4, 249);">'DAS'</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        projectDir = strrep(which(</span><span style="color: rgb(170, 4, 249);">'tutorial_identifyConservedMoieties'</span><span >),</span><span style="color: rgb(170, 4, 249);">'/tutorial_identifyConservedMoieties.mlx'</span><span >,</span><span style="color: rgb(170, 4, 249);">''</span><span >)</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >    </span><span style="color: rgb(14, 0, 255);">case </span><span style="color: rgb(170, 4, 249);">'iDopaNeuro1'</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        projectDir = [</span><span style="color: rgb(170, 4, 249);">'~' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'work' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'sbgCloud' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'programExperimental' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'projects' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'tracerBased'</span><span >]</span></span></div></div><div class="inlineWrapper outputs"><div  class = 'S6'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">end</span></span></div><div  class = 'S7'><div class="inlineElement eoOutputWrapper embeddedOutputsVariableStringElement scrollableOutput" uid="ACE19FCD" data-testid="output_1" data-width="428" data-height="20" data-hashorizontaloverflow="true" style="width: 458px; max-height: 261px; white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div class="textElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><span class="variableNameElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;">projectDir = </span>'/home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/conservedMoieties'</div></div></div></div></div><div class="inlineWrapper outputs"><div  class = 'S10'><span style="white-space: normal"><span >dataDir = [projectDir filesep </span><span style="color: rgb(170, 4, 249);">'data' </span><span >filesep]</span></span></div><div  class = 'S7'><div class="inlineElement eoOutputWrapper embeddedOutputsVariableStringElement scrollableOutput" uid="4CCDF4EB" data-testid="output_2" data-width="428" data-height="20" data-hashorizontaloverflow="true" style="width: 458px; max-height: 261px; white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div class="textElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><span class="variableNameElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;">dataDir = </span>'/home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/conservedMoieties/data/'</div></div></div></div></div><div class="inlineWrapper"><div  class = 'S11'><span style="white-space: normal"><span >addpath(genpath(dataDir));</span></span></div></div><div class="inlineWrapper outputs"><div  class = 'S6'><span style="white-space: normal"><span >softwareDir = [projectDir filesep </span><span style="color: rgb(170, 4, 249);">'software' </span><span >filesep]</span></span></div><div  class = 'S7'><div class="inlineElement eoOutputWrapper embeddedOutputsVariableStringElement scrollableOutput" uid="D3C0BE88" data-testid="output_3" data-width="428" data-height="20" data-hashorizontaloverflow="true" style="width: 458px; max-height: 261px; white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div class="textElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><span class="variableNameElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;">softwareDir = </span>'/home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/conservedMoieties/software/'</div></div></div></div></div><div class="inlineWrapper outputs"><div  class = 'S10'><span style="white-space: normal"><span >visDataDir = [projectDir filesep </span><span style="color: rgb(170, 4, 249);">'data' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'visualisation' </span><span >filesep]</span></span></div><div  class = 'S7'><div class="inlineElement eoOutputWrapper embeddedOutputsVariableStringElement scrollableOutput" uid="73B01DD3" data-testid="output_4" data-width="428" data-height="20" data-hashorizontaloverflow="true" style="width: 458px; max-height: 261px; white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div class="textElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><span class="variableNameElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;">visDataDir = </span>'/home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/conservedMoieties/data/visualisation/'</div></div></div></div></div><div class="inlineWrapper"><div  class = 'S11'></div></div><div class="inlineWrapper outputs"><div  class = 'S6'><span style="white-space: normal"><span >resultsDir = [projectDir filesep </span><span style="color: rgb(170, 4, 249);">'results' </span><span >filesep modelName </span><span style="color: rgb(170, 4, 249);">'_ConservedMoieties' </span><span >filesep]</span></span></div><div  class = 'S7'><div class="inlineElement eoOutputWrapper embeddedOutputsVariableStringElement scrollableOutput" uid="4C55F511" data-testid="output_5" data-width="428" data-height="20" data-hashorizontaloverflow="true" style="width: 458px; max-height: 261px; white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div class="textElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><span class="variableNameElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;">resultsDir = </span>'/home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/conservedMoieties/results/DAS_ConservedMoieties/'</div></div></div></div></div></div><div  class = 'S9'><span>A collection of pre-existing chemical table files in vmh namespace, including atom mapped reactions are here: </span><a href = "https://github.com/opencobra/ctf,"><span>https://github.com/opencobra/ctf,</span></a><span> otherwise use a local directory.</span></div><div class="CodeBlock"><div class="inlineWrapper"><div  class = 'S4'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">switch </span><span >modelName</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >    </span><span style="color: rgb(14, 0, 255);">case </span><span style="color: rgb(170, 4, 249);">'DAS'</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        rxnfileDir = [projectDir filesep </span><span style="color: rgb(170, 4, 249);">'data' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'mini-ctf' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'rxns' </span><span >filesep </span><span style="color: rgb(170, 4, 249);">'atomMapped'</span><span >]</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >    </span><span style="color: rgb(14, 0, 255);">case </span><span style="color: rgb(170, 4, 249);">'iDopaNeuro1'</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        </span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        </span><span style="color: rgb(2, 128, 9);">%rxnfileDir = [resultsDir 'fluxCobra' filesep 'dataBase' filesep 'rxn', filesep 'atomMapped']</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        </span><span style="color: rgb(2, 128, 9);">%rxnfileDir = '~/work/sbgCloud/programReconstruction/projects/exoMetDN/papers/v20/SM/SM5'; %%% temporal</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        </span><span style="color: rgb(2, 128, 9);">%rxnfileDir ='~/work/sbgCloud/data/rxnDatabase/explicitH/atomMapped/RDT/rxnFiles'</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        </span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        </span><span style="color: rgb(2, 128, 9);">%system('git clone git@github.com:opencobra/ctf.git ~/work/sbgCloud/code/fork-ctf/rxns/atomMapped')</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >        rxnfileDir =</span><span style="color: rgb(170, 4, 249);">'~/work/sbgCloud/code/fork-ctf/rxns/atomMapped'</span></span></div></div><div class="inlineWrapper outputs"><div  class = 'S6'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">end</span></span></div><div  class = 'S7'><div class="inlineElement eoOutputWrapper embeddedOutputsVariableStringElement scrollableOutput" uid="F3F8DD84" data-testid="output_6" data-width="428" data-height="20" data-hashorizontaloverflow="true" style="width: 458px; max-height: 261px; white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div class="textElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><div style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;"><span class="variableNameElement" style="white-space: normal; font-style: normal; color: rgb(64, 64, 64); font-size: 12px;">rxnfileDir = </span>'/home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/conservedMoieties/data/mini-ctf/rxns/atomMapped'</div></div></div></div></div><div class="inlineWrapper"><div  class = 'S11'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">if </span><span >~exist(resultsDir,</span><span style="color: rgb(170, 4, 249);">'dir'</span><span >)</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span >    mkdir(resultsDir)</span></span></div></div><div class="inlineWrapper"><div  class = 'S5'><span style="white-space: normal"><span style="color: rgb(14, 0, 255);">end</span></span></div></div><div class="inlineWrapper"><div  class = 'S12'><span style="white-space: normal"><span >cd(resultsDir)</span></span></div></div></div><div  class = 'S9'><span>Decide whether to recompute everything from scratch or try to load cached intermediate results</span></div><div class="CodeBlock"><div class="inlineWrapper"><div  class = 'S13'><span style="white-space: normal"><span >recompute = 1;</span></span></div></div></div>
<br>
<!-- 
##### SOURCE BEGIN #####
%% Initialisation of conserved moiety decomposition
% Conserved moiety decomposition consists of several sequential live scripts
%% 
% # tutorial_initConservedMoietyPaths.mlx   (this script)
% # tutorial_buildAtomTransitionMultigraph.mlx                                
% # tutorial_identifyConservedMoieties.mlx
% # tutorial_analyseConservedMoieties.mlx
% # tutorial_visualiseConservedMoieties.mlx     
%% 
% Define the model that will be used for conserved moiety decomposition

if ~exist('modelName','var')
    modelName = 'iDopaNeuro1';
    %modelName = 'DAS'
end
%% 
% Setup the paths

switch modelName
    case 'DAS'
        projectDir = strrep(which('tutorial_identifyConservedMoieties'),'/tutorial_identifyConservedMoieties.mlx','')
    case 'iDopaNeuro1'
        projectDir = ['~' filesep 'work' filesep 'sbgCloud' filesep 'programExperimental' filesep 'projects' filesep 'tracerBased']
end
dataDir = [projectDir filesep 'data' filesep]
addpath(genpath(dataDir));
softwareDir = [projectDir filesep 'software' filesep]
visDataDir = [projectDir filesep 'data' filesep 'visualisation' filesep]

resultsDir = [projectDir filesep 'results' filesep modelName '_ConservedMoieties' filesep]
%% 
% A collection of pre-existing chemical table files in vmh namespace, including 
% atom mapped reactions are here: <https://github.com/opencobra/ctf, https://github.com/opencobra/ctf,> 
% otherwise use a local directory.

switch modelName
    case 'DAS'
        rxnfileDir = [projectDir filesep 'data' filesep 'mini-ctf' filesep 'rxns' filesep 'atomMapped']
    case 'iDopaNeuro1'
        
        %rxnfileDir = [resultsDir 'fluxCobra' filesep 'dataBase' filesep 'rxn', filesep 'atomMapped']
        %rxnfileDir = '~/work/sbgCloud/programReconstruction/projects/exoMetDN/papers/v20/SM/SM5'; %%% temporal
        %rxnfileDir ='~/work/sbgCloud/data/rxnDatabase/explicitH/atomMapped/RDT/rxnFiles'
        
        %system('git clone git@github.com:opencobra/ctf.git ~/work/sbgCloud/code/fork-ctf/rxns/atomMapped')
        rxnfileDir ='~/work/sbgCloud/code/fork-ctf/rxns/atomMapped'
end
if ~exist(resultsDir,'dir')
    mkdir(resultsDir)
end
cd(resultsDir)
%% 
% Decide whether to recompute everything from scratch or try to load cached 
% intermediate results

recompute = 1;
##### SOURCE END #####
-->
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